PeaksToPathways_highvslowrisk_tscore_FINAL_clean.csv (730.2 KB)
PeaksToPathways_highvslowrisk_tscore.txt (730.2 KB)
Hello, My files for Pathway analysis are uploaded with this question. Can you please review and tell me the error? I think these are clean and align with the IBD2 example set.
Sorry for asking this elementary question.
thank you
Vidhu
Yes, I can see they are both OK, and also worked as expected (see below). Can you clarify what issue you experienced when you upload?
Thanks for the reply. Can you please try the mixed mode to see if it works for you? I have HILIC positive and C18 negative data in the sheet. Is it inappropriate to use mixed mode?
Mixed mode refers to positive & negative modes for the same column type. If you mix different columns, their retention times will not be comparable
Thank you for the response. Does this mean that I should upload HILIC positive and C18 negative separately? Does this also apply to RNA seq and metabolomics joint pathway analysis?
You can certainly upload and analyze HILIC positive and C18 negative separately - which is the default. Note we discussed several data integration strategies for meta-analysis or systems biology in our Omics Data Science course
- (low-level) Feature level integration
=> require data generated from the same sample from the same instrument - (middle) Compound level integration
=> require data generated from same samples. You annotate the data to compounds, and then combine them. This applies to different LC-MS instruments - (high) Pathway level integration
=> require data generated from the same tissue / individual. This applies to RNAseq and metabolomics integration